Clashes between Muslims and Christians in the Egyptian capital, Cairo, have left 11 people dead and more than 90 wounded.

The clashes broke out on Tuesday night as thousands of Christians protested against the burning of a Cairo church last week. The church was set on fire after tensions escalated over a love affair between a Muslim and a Christian that set off a violent feud between the couple's families.

Security and hospital officials said six Christians and five Muslims died from gunshot wounds and 94 people – 73 Muslims and 21 Christians – were wounded.

Christian protesters blocked a highway, burning tyres and pelting cars with rocks. The two sides fought pitched battles for about four hours.

The 18-day uprising that toppled the president, Hosni Mubarak, on 11 February has left a security vacuum. Police pulled out of Cairo and several other cities three days into the uprising and have yet to fully take back the streets.

Mubarak handed power to the military when he stepped down, but it does not have enough troops to police every street in Cairo.

Egypt's ruling generals pledged last week to rebuild the burned church. The country's new prime minister, Essam Sharaf, has met Christian protesters in central Cairo to reassure them they would not face discrimination from his interim government.

However, at least 2,000 Christians joined the protest on Tuesday and a separate crowd of several hundred has been camping out outside the TV building for days to voice their anger at what they perceive to be official discrimination against them.